FPGA implementation of a data-driven stochastic biochemical simulator with the next reaction method

Masato Yoshimi, Yow Iwaoka, Yuri Nishikawa, Toshinori Kojima, Yasunori Osana, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hideki Yamada, Hiroaki Kitano, Hideharu Amano

Research output: Chapter in Book/Report/Conference proceedingConference contribution

13 Citations (Scopus)

Abstract

This paper introduces a scalable FPGA implementation of a stochastic simulation algorithm (SSA) called the Next Reaction Method. There are some hardware approaches of SSAs that obtained high-through put on reconfigurable devices such as FPGAs, but these works lacked in scalability. The design of this work can accommodate to the increasing size of target biochemical models, or to make use of increasing capacity of FPGAs. Interconnection network between arithmetic circuits and multiple simulation circuits aims to perform a data-driven multi-threading simulation. Approximately 8 times speedup was obtained compared to an execution on Xeon 2.80GHz.

Original languageEnglish
Title of host publicationProceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL
Pages254-259
Number of pages6
DOIs
Publication statusPublished - 2007
Externally publishedYes
Event2007 International Conference on Field Programmable Logic and Applications, FPL - Amsterdam, Netherlands
Duration: 2007 Aug 272007 Aug 29

Other

Other2007 International Conference on Field Programmable Logic and Applications, FPL
CountryNetherlands
CityAmsterdam
Period07/8/2707/8/29

Fingerprint

Field programmable gate arrays (FPGA)
Simulators
Circuit simulation
Scalability
Hardware
Networks (circuits)

ASJC Scopus subject areas

  • Computer Science Applications
  • Electrical and Electronic Engineering

Cite this

Yoshimi, M., Iwaoka, Y., Nishikawa, Y., Kojima, T., Osana, Y., Funahashi, A., ... Amano, H. (2007). FPGA implementation of a data-driven stochastic biochemical simulator with the next reaction method. In Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL (pp. 254-259). [4380656] https://doi.org/10.1109/FPL.2007.4380656

FPGA implementation of a data-driven stochastic biochemical simulator with the next reaction method. / Yoshimi, Masato; Iwaoka, Yow; Nishikawa, Yuri; Kojima, Toshinori; Osana, Yasunori; Funahashi, Akira; Hiroi, Noriko; Shibata, Yuichiro; Iwanaga, Naoki; Yamada, Hideki; Kitano, Hiroaki; Amano, Hideharu.

Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL. 2007. p. 254-259 4380656.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Yoshimi, M, Iwaoka, Y, Nishikawa, Y, Kojima, T, Osana, Y, Funahashi, A, Hiroi, N, Shibata, Y, Iwanaga, N, Yamada, H, Kitano, H & Amano, H 2007, FPGA implementation of a data-driven stochastic biochemical simulator with the next reaction method. in Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL., 4380656, pp. 254-259, 2007 International Conference on Field Programmable Logic and Applications, FPL, Amsterdam, Netherlands, 07/8/27. https://doi.org/10.1109/FPL.2007.4380656
Yoshimi M, Iwaoka Y, Nishikawa Y, Kojima T, Osana Y, Funahashi A et al. FPGA implementation of a data-driven stochastic biochemical simulator with the next reaction method. In Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL. 2007. p. 254-259. 4380656 https://doi.org/10.1109/FPL.2007.4380656
Yoshimi, Masato ; Iwaoka, Yow ; Nishikawa, Yuri ; Kojima, Toshinori ; Osana, Yasunori ; Funahashi, Akira ; Hiroi, Noriko ; Shibata, Yuichiro ; Iwanaga, Naoki ; Yamada, Hideki ; Kitano, Hiroaki ; Amano, Hideharu. / FPGA implementation of a data-driven stochastic biochemical simulator with the next reaction method. Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL. 2007. pp. 254-259
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